I have upgraded from 13.04 to 13.10 today and everything works smooth apart from one thing. I have a dual monitor setup and every time reboot the screens have switched places (left screen on right monitor and vice versa).
I have correctly created an xorg.conf which is shown below.

I have tried all the solutions which are suggested in theses two posts:

including checking for ~/.config/monitor.xml which I don't have. Loading the nvidia-setting at runtime using nvidia-settings -l which doesn't do anything. But that kinda makes sense to me since the .nvidia-setting-rc doesn't really have any info about screen positions. And since I'm running LXDE as my desktop environment "Preferences->Monitor Settings" is only concerned with screen resolution, not screen position.

Now here is the odd thing: When lightdm loads up the screens are initially in the correct order (as specified in the xorg.conf) and then switch order after a couple of secounds.

which I believe could very well be the culprit. It seems as if the nvidia driver overrides the settings in xorg.conf after the fact even though I'm not starting nvidia-settings at startup as far as I know.

EDIT:

I just upgraded from nvidia-304 to nvidia-319 and now my suspicions a confirmed because the x-server boot log is now a little bit clearer. The relevant lines are:

What I found out is that the log message which signals the override of the xorg.conf settings is one that is caused by a call to xrandr (as I'm doing this myself from the commandline to set the screens in the correct order).

Below you'll find my x-server log file. Please be aware that the very last two entries at approx. 31.5 secs are caused by me calling xrandr from the commandline with the correct settings.

Just a guess, but does the same thing happen if you login with gdm
– Amith KKFeb 19 '14 at 2:34

could you change all the "DFP-1" to "DFP" and all "CRT-0" to "CRT"? the later are more general.
– t4lwhFeb 19 '14 at 5:40

@AmithKK I don't see how the login manager could determine the screen order. That falls into the responsibility of the x-server.
– CorneliusFeb 19 '14 at 17:57

@timl I tried it but no change. But like it said, it seems the xorg.conf is read in and orders the screens in the right order but afterwards the nvidia driver kicks in and overrides the xorg settings with its own defaults.
– CorneliusFeb 19 '14 at 17:58

do you mean after you changed them, nvidia will override xorg.conf again? the changes was meant to be decide the order like 'all DFP first, then CRT'. because the 'DFP-1, CRT-0' still may become 'DFP-1 first, CRT-0 second, other DFP again, then other CRT'. wild guess for 'why screens get switched' ;)
– t4lwhFeb 20 '14 at 2:16

Or, as I found out, you could just delete ~/.config/monitors.xml altogether
– Giorgos KylafasApr 3 '17 at 6:57

Furthermore , adding to this answer and to Giorgos comment, according to this bug report answers.launchpad.net/ubuntu/+source/xorg/+question/254081 if that bug is still here, which i think it is, while watching my ~/.config/monitors.xml and my /etc/X11/xorg.conf i realised that nvidia is trying to load a different screen frequency refresh rate from the gnome setting. So right now the best option is to delete that setting in monitors.xml so that it doesn't override the nvidia one. Good finding. Now i don't need to make a script to run nvidia settings later after boot.
– Pavlos TheodorouNov 12 '18 at 7:31

The issue seems to be, that lightdm resets the screens to an order it sees fit after the xorg.conf has been loaded. (I don't now why or how to suppress that and would find it helpful if some could shed some light on that.)

So to solve this issue the simple solution is to change the display manager. See here

The more complicated solution if you want to keep lightdm is to install arandr. Run it. Set your screens up like you want them and save the configuration. This will save a shell script which sets up your configuration whenever it is executed. So now you have to add the following line to /etc/lightdm/lightdm.conf

session-setup-script=<location of the script you saved with arandr>

This will get you the correct monitor setup as soon as you enter you session.

This doesn't work for me. Ubuntu 16.04. I can see after lightdm restart that briefly it is correct, but in a fraction of seconds screen blink and monitors are replaced in order again.
– omikronDec 20 '16 at 10:50

I had a similar issue - not multi-monitor, but my settings were getting ignored like yours are. What I did to solve it was replace the nvidia-auto-select option with the actual resolution I wanted, i.e. 1280x1024_75 +0+0.

Additionally, I noticed that in the above line, the monitors are in the order "CRT-0, DFP-1", whereas earlier in your config file they're ordered "DFP-1, CRT-0". I don't know if that matters, but these flip-flops may also be causing your issue, so try setting everything in the same order.

What I think was happening for me was that the nvidia x-server would load its preferred settings, then would be overridden by the settings manager. By removing the auto-select (and any other resolution options available in /etc/X11/xorg.conf) I think it disallows the use of other resolution settings.

Thanks for the idea, but what matters are the screen resoluiton offsets (i.e. +1680+0) and they but the CRT to the left of the DFP. Also I'm sure now the issue is not in the xorg.conf but something is issuing a call to xrandr after xorg.conf has been loaded (see EDIT2).
– CorneliusFeb 22 '14 at 9:21

That just creates a xorg.conf which I already created via the nvidia-settings tool. Also I would created with default settings, meaning the screens would end up in the wrong order.
– CorneliusFeb 19 '14 at 17:52

For xfce4 users, it looks like the file ~/.config/xfce4/xfconf/xfce-perchannel-xml/displays.xml could have been modified for some reason. Deleting it solved my issue. It's not been generated again at logout/login so I don't know exactly what it is supposed to do. I also found that with other desktop environments there is a similar(?) ~/.config/monitors.xml file that you might try deleting/renaming.